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GATK Dev Team

@gatk_dev

@davemc528 No, we don’t trim reads in any of our short read pipelines. Happy to discuss in more detail and point yo… https://t.co/QWMPXegkY0
13 Dec 19
@HollyMcQueary In general that sounds appropriate, though this might be worth discussing in more detail in our supp… https://t.co/5sa0D9iHkY
11 Dec 19
@FanBoyShi For this kind of question we'd prefer you post in the forum so we can troubleshoot in detail -- but if… https://t.co/bQqUp4ZInM
8 Dec 19


Solutions to Problems

Tips for solving common problems and errors


Allele Depth (AD) is lower than expected
AnalyzeCovariates fails with error message "RScript exited with 1"
Errors about contigs in BAM or VCF files not being properly ordered or sorted
Errors about input files having missing or incompatible contigs
Errors about misencoded quality scores
Errors about read group (RG) information
Errors in SAM/BAM files can be diagnosed with ValidateSamFile
I am unable to use VQSR (recalibration) to filter variants
I do not get the annotations I specified with -A
I expect to see a variant at a specific site, but it's not getting called
I need to run programs that require different versions of Java
 
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